I never did find an empty flask for the swamp water. Where the heck is it?

I think you should find a few around the place, usually at quest locations. An old friend should give you a couple when you find them too, might just have to search a bit more ;)

I never had any trouble finding more flasks than you need, so I can't remember where you find them. However, if you're really having trouble, you can always buy a second vial of earth powder from Sadie, have one of your characters eat the earth powder (it's gross, but it won't kill him), and then use the resulting empty flask to get the swamp water.

Their are multiple empty vials in the game. One can be found in the Draracle's Cave, another 2 deep in the Urbish Mines, and another given by Dawn. You only need two (one for the honey, one for the swamp water).